ABSTRACT Circadian rhythms controlled by intrinsic biological clocks enable anticipatory changes in cellular physiology to promote adaptation to daily environmental cycles. The pervasiveness of circadian programs among eukaryotes and cyanobacteria suggests that circadian clocks confer a fitness advantage to organisms exposed to fluctuating growth environments. Despite the ubiquity of circadian clocks, the specific benefits of circadian systems to overall fitness have remained elusive. Previous studies in the model cyanobacterium Synechococcus elongatus PCC 7942 demonstrated that cyanobacteria whose circadian period closely matches the external light cycle are more fit than strains with periods that differ. Importantly, these studies relied on mutants with defective core clocks, which resulted in previously unappreciated pleiotropic consequences. Here, we propose to test the fitness benefit of circadian rhythms in cyanobacteria using a strain that is unable to produce oscillations in gene expression despite possessing an intact circadian clock, in order to avoid biases encountered by clock mutants. The previously described crm1 mutant contains a transposon insertion in the crm (circadian rhythmicity modulator) ORF that results in arrhythmic expression of clock controlled genes. The crm1 allele elicits phenotypes distinct from arrhythmic kaiC-null and rpaA-null strains, and the crm1 mutant grows in alternating light-dark cycles, providing a strain with moderate arrhythmic gene expression ideal for fitness studies. Competition experiments between the arrhythmic crm1 mutant and WT or other arrhythmic mutants, coupled with metabolic profiles and high-throughput TnSeq-based genetic interaction screens in the crm1 background, will improve our understanding of the fitness consequences encountered by cyanobacteria that fail to maintain rhythmic gene expression. Furthermore, this work is intended to characterize the RpaA-modulating activity of the enigmatic Crm peptide, adding to our model of factors that influence clock output. Taken together, this work has the potential to inform future studies regarding clock-controlled fitness in humans. It is becoming increasingly apparent that the toll of modern life ? including shiftwork, blue-light exposure, jet travel and other behaviors ? can profoundly disrupt circadian programs in a variety of mammalian tissues, contributing to disease. Our ability to assess the fitness advantage of biological clocks in mammalian tissues is limited, necessitating tractable model organisms such as S. elongatus to investigate fitness components of the clock network. The work may provide a framework for future understanding and treatment of circadian disruption in humans.